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This page was generated on 2015-10-27 12:12:43 -0400 (Tue, 27 Oct 2015).
| Package 424/1104 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| GenomicInteractions 1.5.0 Malcolm Perry
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | ||||||
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK |
| Package: GenomicInteractions |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.5.0.tar.gz |
| StartedAt: 2015-10-27 04:13:58 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 04:17:42 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 224.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenomicInteractions.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicInteractions.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.5.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicInteractions’ can be installed ... [18s/18s] WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘Gviz::availableDisplayPars’ when loading ‘GenomicInteractions’
See ‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicInteractions.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 10.8Mb
sub-directories of 1Mb or more:
doc 1.6Mb
extdata 7.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’ ‘GenomeInfoDb:::getDanglingSeqlevels’
‘GenomeInfoDb:::makeNewSeqnames’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Annotating with promoter ...
testthat results ================================================================
OK: 75 SKIPPED: 0 FAILED: 1
1. Error: bed12 export/import is consistent
Error: testthat unit tests failed
In addition: Warning messages:
1: In calculateDistances(gi, method = "inner") :
setting negative distances to 0, this is due to the presence of overlapping anchors in your dataset
2: In calculateDistances(gi, method = "inner") :
setting negative distances to 0, this is due to the presence of overlapping anchors in your dataset
3: Removed 1 rows containing missing values (geom_text).
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.
GenomicInteractions.Rcheck/tests/testthat.Rout.fail:
R Under development (unstable) (2015-09-09 r69333) -- "Unsuffered Consequences"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(GenomicInteractions)
Warning message:
replacing previous import by 'Gviz::availableDisplayPars' when loading 'GenomicInteractions'
>
> test_check("GenomicInteractions")
Annotating with promoter ...
1. Error: bed12 export/import is consistent ------------------------------------
The "ifelse" methods for Rle objects are defunct. Please use
as(ifelse(test, as.vector(yes), as.vector(no)), "Rle")
instead.
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: export.bed12(gi, fn = tmp) at test_import.R:36
5: export.bed12(gi, fn = tmp)
6: data.frame(chr = as.character(seqnames(anchorOne(cis))), start = start(anchorOne(cis)) -
1, end = end(anchorTwo(cis)), name = .exportName(cis), score = interactionCounts(cis),
strand = ifelse(s1 == s2 & s1 %in% c("+", "-"), s1, "."), thickStart = start(anchorOne(cis)) -
1, thickEnd = end(anchorTwo(cis)), itemRgb = rep("255,0,0", len), blockCount = 2,
blockSizes = paste(as.character(width(anchorOne(cis))), as.character(width(anchorTwo(cis))),
sep = ","), blockStarts = paste(0, start(anchorTwo(cis)) - start(anchorOne(cis)),
sep = ","))
7: ifelse(s1 == s2 & s1 %in% c("+", "-"), s1, ".")
8: ifelse(s1 == s2 & s1 %in% c("+", "-"), s1, ".")
9: .Defunct(msg = .ifelse_generic_defunct_msg)
10: stop(paste(msg, collapse = ""), call. = FALSE, domain = NA)
Annotating with promoter ...
testthat results ================================================================
OK: 75 SKIPPED: 0 FAILED: 1
1. Error: bed12 export/import is consistent
Error: testthat unit tests failed
In addition: Warning messages:
1: In calculateDistances(gi, method = "inner") :
setting negative distances to 0, this is due to the presence of overlapping anchors in your dataset
2: In calculateDistances(gi, method = "inner") :
setting negative distances to 0, this is due to the presence of overlapping anchors in your dataset
3: Removed 1 rows containing missing values (geom_text).
Execution halted
GenomicInteractions.Rcheck/00install.out:
* installing *source* package ‘GenomicInteractions’ ... ** R ** data ** inst ** preparing package for lazy loading Warning: replacing previous import by ‘Gviz::availableDisplayPars’ when loading ‘GenomicInteractions’ Creating a generic function for ‘print’ from package ‘base’ in package ‘GenomicInteractions’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import by ‘Gviz::availableDisplayPars’ when loading ‘GenomicInteractions’ * DONE (GenomicInteractions)
GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings:
| name | user | system | elapsed | |
| GenomicInteractions-class | 0.127 | 0.000 | 0.128 | |
| GenomicInteractions | 0.094 | 0.000 | 0.094 | |
| InteractionTrack | 0.631 | 0.032 | 0.664 | |
| annotateInteractions | 0.399 | 0.012 | 0.412 | |
| calculateDistances | 0.135 | 0.000 | 0.135 | |
| categoriseInteractions | 0.059 | 0.000 | 0.058 | |
| getters | 0.101 | 0.000 | 0.101 | |
| makeGenomicInteractionsFromFile | 1.406 | 0.012 | 1.419 | |
| plotCisTrans | 0.573 | 0.000 | 0.573 | |
| plotCounts | 0.218 | 0.008 | 0.227 | |
| plotDists | 0.147 | 0.020 | 0.167 | |
| plotInteractionAnnotations | 0.181 | 0.000 | 0.182 | |
| plotSummaryStats | 0.668 | 0.004 | 0.674 | |
| setters | 0.142 | 0.008 | 0.150 | |
| unique-GenomicInteractions-method | 0.206 | 0.000 | 0.206 | |
| viewPoint | 0 | 0 | 0 | |